rs17171989

Variant names:

• chr7-41947526-G-A
• rs17171989

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.402 in 151,742 control chromosomes in the GnomAD database, including 13,884 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (13884 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60837 AN: 151624 Hom.: 13843 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.386

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.402 AC: 60939 AN: 151742 Hom.: 13884 Cov.: 31 AF XY: 0.395 AC XY: 29308 AN XY: 74170

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.392

Alfa AF: 0.338 Hom.: 4317

Bravo AF: 0.412

Asia WGS AF: 0.422 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17171989; hg19: chr7-41987124;